I know at the moment if the shedship or chinook areas intersect with a sub-map (even if it's just by one tile) then the entire sub-map is completely removed.
I figured that the UFOs and transports would all be on the same sized sub-maps, but smaller UFOs would have more random items around them (signs, wreckage, barrels, fencing, paving, broken structures etc). So you could randomly end up with a UFO half embedded in a building, but it wouldn't actually insert it into pre-existing stuff on the map. As pointed out though, this probably wouldn't work for really large ships as it would mean the smallest ships would need heaps of random stuff around them and that might lead to combinations that look out of place on some maps.